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I've just watched Alien: Covenant. I watched Prometheus quite a while back but don't fully remember the story, so I couldn't exactly relate the two movies. But from what I can tell, Covenant is just a continuation of Prometheus.
Could someone please explain the story in detail? Specially, who is/are ‘Prometheus’ and how are they related to the Aliens? Were the Aliens created by nature or were they created by us? (In Covenant David says that we spread the virus on the Prometheus planet.)
‘Prometheus’ is the space ship in the movie Prometheus which, based on ancient star maps discovered on earth, travels to the distant moon LV-223 (note: not LV-426, which we see in Alien and Aliens) in hope of finding an alien intelligence (the ‘Engineers’) that may have created life on earth.
In Prometheus, the crew discovers what appears to be a scientific or military installation belonging to the Engineers, with almost all of the inhabitants long since killed by creatures created by their own experiments with a black oily substance. Of the Prometheus crew
only one human (Elizabeth Shaw) and one android (David) survive. They take control of an Engineer ship, and set course for what they believe to be the Engineer home world.
(Wikipedia covers this quite well.)
In Alien: Covenant, the colonisation ship ‘Covenant’ lands on this same world, and the crew encounter David. Eventually, it’s revealed that
David released the black substance on the planet’s Engineer population before landing the ship, killing them all. He then spent years performing genetic experiments, including on Elizabeth Shaw, which culminated in his creation of what look very much like facehuggers, and subsequently a fully-grown alien, from the original Alien movie.
The xenomorphs were created as the result of the Engineer's morphic goo -- but not by the engineers. The goo promotes a sort of hyper-evolution within any organism it comes into contact with.
In the beginning of Prometheus we see the goo used as a means for promoting life - where an engineer eats the goo and, with his sacrificial self, seeds life on... our primordial Earth.
The xenomorph is a weaponized version of an infected species - built using the infected species' own DNA; but whether that weaponized result was intended by the originating engineers, or not, is not disclosed.
Humans, looking for their Creators (the engineers), arrive aboard Prometheus on LV-223.
The engineers on LV-223 are all dead except for one who is in stasis. Evidently they had a sort of civil war or techo-disaster concurrent with some of them making idols of and worshiping... someone who looks like themselves. There's a hologram that shows some engineers running from something; but it's a mystery what they were running from in the hologram.
Accompanying the humans in Prometheus is a self-worshiping android named David -- and he makes things worse - for everybody.
It is David who, along with Dr. Shaw, escapes from LV-223 to an unnamed planet inhabited by humanoids having an appearance similar to the engineers. It is also David who, upon arrival on the unnamed planet, releases the black goo and genocides the humanoid engineeresque inhabitants.
David, while marooned alone on the unnamed planet, "creates" the xenomorphs after studying and using the goo to manifest his own insane vision -- culminating with the familiar eggs and face-huggers.
The Covenant is a colony ship that is lured into going off course to investigate a radio signal of someone singing John's Denver's "country road" emanating from David's unnamed, unknown, uncharted planet.
The first human host seeded by David's face-hugger is the faithful captain of the Covenant.
